// get_arg.h
//

#if !defined(GETARG_H)
#define GETARG_H

#include <string>
#include <sstream>
#include <fstream>
#include <iostream>
#include <bcpp_seq_formats.h>


#include <program_options_helper.h>

class t_program_args : public program_options_helper::t_std_program_args_with_errors
{
public:
	// for initializing this struct
	friend
	bool process_command_line_options(int argc, char* argv[], t_program_args& args);
	BioCPP::eSEQ_FORMAT		input_format;
	BioCPP::eSEQ_FORMAT		output_format;
	bool					header;
	std::string				regex;
	std::string				file_input;
    std::string				file_names;
    std::string             file_map_to_short_names;
	std::vector<unsigned>	pos_indices;
	unsigned				line_wrap;
	bool					alpha;
	bool					names;

};

bool process_command_line_options(int argc, char* argv[], t_program_args& args);
#endif //GETARG_H

